Re: [ccp4bb] How to apply correction factors for translational NCS in PHASER?

2013-10-23 Thread Randy J. Read
Hi,

If there is more than one strong unique Patterson peak, then Phaser currently 
doesn't know how to interpret the tNCS. If all the peaks can be interpreted as 
multiples of one one vector (taking symmetry into account) then you can use the 
NMOL argument of the tNCS command. Otherwise, you can get Phaser to only take 
account of the top peak by setting the minimum peak height. 

If you post or email the list of peaks, I might be able to give some specific 
advice (although I'll be on my way to the Cold Spring Harbor school most of the 
day). 

Best wishes,

Randy Read


Randy J. Read

 On 22 Oct 2013, at 23:35, Niu Tou niutou2...@gmail.com wrote:
 
 Dear All,
 
 I have a MR case which may contain two different molecules, ideally 1:1 
 ratio. Solvent content analysis indicates most likely to be 4~6 hetero 
 molecules. The data shows at least 5 strong translational NCS vectors. 
 
 When I tried to run PHASER, it always said correction factors NOT applied, 
 but I have chosen to count it in the interface. Is there anyway I could use 
 these NCS information, either by checking some options in the GUI of 
 modifying the script? Many thanks!
 
 Best,
 Niu 


[ccp4bb] stereo monitors/MAC

2013-10-23 Thread Adrian Goldman
Hi,

Having now had a chance (finally) to play with the Asus VG27A, I can 
say that (a) it works really well in stereo with both Coot and PyMol and (b) it 
is easier and nicer to use than the Zalmans.

Though the technology is essentially the same (halving the vertical 
resolution), they have done two things better than the Zalmans:
1) - they don't just eliminate Pixels in the non-stereo sections of the screen 
like the menus.  The menus become less easy to read (and completely weird in 
mono) but they can be read in stereo.  This is a GOOD THING.

2) - there is a handy-dandy button at the bottom of the display that switches 
the screen into stereo from mono, and works fine in both coot and pymol.

Heartily recommended for the 
diehards who like having the z-coordinates of their models correct.


adrian

[ccp4bb] Structural Biology Faculty Position at Purdue University

2013-10-23 Thread Andrew Mesecar
* *

Faculty Position in Structural Biology

Purdue University



The Department of Biological Sciences and the Markey Center for Structural
Biology at Purdue University invite applications for a tenure-track faculty
position in Structural Biology. We expect to fill this academic-year
appointment at the Assistant Professor level, but appointment at the
Associate level will also be considered.  Applicants must have a Ph.D. or
equivalent in biology, chemistry, physics or related field and at least 2
years of postdoctoral experience in X-ray crystallography, cryo-EM, NMR or
other relevant field. The successful applicant will be required to
establish a strong and independent research program in structural biology
and to teach at the undergraduate and graduate levels.  Applicants with
research interests in cancer biology, drug discovery, energy  signal
transduction, infectious disease, large macromolecular complexes,
membrane-based transport, molecular pathogenesis, neurobiology, viruses or
viral-host interactions are encouraged to apply.



The Markey Center for Structural Biology at Purdue is recognized worldwide
for its leadership in structural biology of viruses, membrane proteins,
receptors, signaling proteins and enzymes in addition to methods
development in crystallography, NMR and electron microscopy.  The
Department has over 50 faculty members conducting research in a wide range
of fields including those areas listed above, bioinformatics, computational
chemistry and biology, ecology, evolutionary biology and vision research.
The successful candidate will have opportunities to interact with
colleagues in many departments and colleges including Chemistry, Medicinal
Chemistry and Molecular Pharmacology, Computer Science and Physics, and to
join centers such as the Center for Cancer Research and the new Center for
Drug Discovery.  The successful candidate will also have laboratory space
in the newly constructed Hockmeyer Hall of Structural Biology and will have
access to state-of-the-art shared resources across Purdue including a Titan
Krios cryo-TEM, Bruker Avance-III 800 MHz NMR, Rigaku X-ray generators and
detectors, and other advanced biophysical instrumentation available at the
Bindley Bioscience Center and the Birck Nanotechnology Center.



Applications must be submitted electronically to *sea...@bio.purdue.edu* as
a PDF file that includes a detailed curriculum vitae, names and addresses
of three referees, a 2 - 3 page summary of research interests, and a
one-page statement on a vision for teaching.  Inquiries should be directed
to *Structural Biology Search Committee, Department of Biological Sciences,
Purdue University, 915 W. State St., West Lafayette, IN 47907-2054*.  Review
of applications will begin *November 1, 2013 *and continue until the
position is filled. Further information about the Department is available
at http://www.bio.purdue.edu/.



* *

*Purdue University in an Equal Opportunity/Equal Access/Affirmative Action
employer fully committed to achieving a diverse workforce.*


[ccp4bb] stereo monitors/MAC (try 3!)

2013-10-23 Thread Adrian Goldman
Hi,

(and apologies if ANYONE has seen this twice - CCP4BB rejected my first 
post as coming from an unknown (i.e. Leeds) address, and the second one because 
I had already posted from my Leeds address….)

Here goes:

Having now had a chance (finally) to play with the Asus VG27A, I can 
say that (a) it works really well in stereo with both Coot and PyMol and (b) it 
is easier and nicer to use than the Zalmans.

Though the technology is essentially the same (halving the vertical 
resolution), they have done two things better than the Zalmans:
1) - they don't just eliminate Pixels in the non-stereo sections of the screen 
like the menus.  The menus become less easy to read (and completely weird in 
mono) but they can be read in stereo.  This is a GOOD THING.

2) - there is a handy-dandy button at the bottom of the display that switches 
the screen into stereo from mono, and works fine in both coot and pymol.

Heartily recommended for the 
diehards who like having the z-coordinates of their models correct.


adrian

Re: [ccp4bb] membrane protein optimization

2013-10-23 Thread Dr. Isabel De Moraes
Dear  Frank,

It is difficult to say something without the diffraction images but  probably 
they are detergent ( or lipid) crystals.  These crystals are in general soft 
and don't diffract well.

My suggestion is to know well what your crystals really are before any 
optimization.

Best,
Isabel

Dr Isabel De Moraes, MRSC

Membrane Protein Laboratory
Diamond Light Source Ltd,
Harwell Science and Innovation Campus,
Chilton, Didcot, Oxfordshire,
OX11 ODE, UK




On 23 Oct 2013, at 17:22, crystalboy wrote:

 Hi CCP4BB Forks,

 In recently I got a membrane protein crystal in the quite normal
 membrane protein crystallization conditions as other persons reported,
 like PEG400 16-19%, pH 6.0-7.5, with 50 mM MgCl2 (in my case) by using
 sitting drop method. These crystals are around 50-100 uM. They look
 like trapezoid crystal. My problem is all of my crystals have not
 diffraction in home source X-ray and just poor diffraction at
 Synchrotron (lower than 20 A). My crystals like to appear on the
 surface of the drop. Look like my crystals are quite light.  I had
 tried to use a needle to touch them. Unlike other protein crystal, my
 crystal looks like quite soft. When I touch it, it didn't crack, but
 was bend or mashed.  I had tried to do additive screen and detergent
 screen. It seems they are not useful.

 Do anyone have good ideas to optimization these crystals? Thanks for
 your suggestions.

 Frank
[cid:7839c9ff-b567-4b4b-b191-07dc6c335f34@fed.cclrc.ac.uk]




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please notify us of receipt by returning the e-mail and do not use, copy, 
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Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 

Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
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the message.

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Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

 









Re: [ccp4bb] membrane protein optimization

2013-10-23 Thread Bert Van-Den-Berg
The problem you're having is a very common one, unfortunately. There are about 
10,000 things you can try to improve diffractiongenerally going from low to 
solvable resolution is very, very hard.
I would say the two most important ones are (i) to vary the detergent and (ii) 
to go to another homolog if (i) doesn't work. You don't mention which detergent 
you're using (DDM?), but the best chance of success would be to try harsher 
detergents, ie those that form small micelles (shorter chain maltosides, b-OG, 
LDAO etc). Give bicelles a try too, and LCP if you know someone with an LCP 
robot. If your protein is stable only in DDM you're out of luck and the best 
thing would be to look for an ortholog that is more stable.

Good luck, Bert



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of crystalboy 
[yyb...@gmail.com]
Sent: Wednesday, October 23, 2013 5:22 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] membrane protein optimization

Hi CCP4BB Forks,

In recently I got a membrane protein crystal in the quite normal
membrane protein crystallization conditions as other persons reported,
like PEG400 16-19%, pH 6.0-7.5, with 50 mM MgCl2 (in my case) by using
sitting drop method. These crystals are around 50-100 uM. They look
like trapezoid crystal. My problem is all of my crystals have not
diffraction in home source X-ray and just poor diffraction at
Synchrotron (lower than 20 A). My crystals like to appear on the
surface of the drop. Look like my crystals are quite light.  I had
tried to use a needle to touch them. Unlike other protein crystal, my
crystal looks like quite soft. When I touch it, it didn't crack, but
was bend or mashed.  I had tried to do additive screen and detergent
screen. It seems they are not useful.

Do anyone have good ideas to optimization these crystals? Thanks for
your suggestions.

Frank


Re: [ccp4bb] membrane protein optimization

2013-10-23 Thread Susanne Ressl
Hi Frank,

unfortunately it is very common with membrane protein crystals to get stuck 
with diffraction quality around 20A.

From what you describe you could consider the following:

a) revise the detergent you solubilize your MP with (e.g. use OG instead of 
DDM), and consider to change to another (shorter) detergent that might allow 
tighter crystal packing
b) engineer your MP,mutate charged residues to alanine (check function!)
c) try homolog protein
d) try to crystallize in lipid cubic phase

Best of luck!
Susanne

On Oct 23, 2013, at 9:22 AM, crystalboy wrote:

 Hi CCP4BB Forks,
 
 In recently I got a membrane protein crystal in the quite normal
 membrane protein crystallization conditions as other persons reported,
 like PEG400 16-19%, pH 6.0-7.5, with 50 mM MgCl2 (in my case) by using
 sitting drop method. These crystals are around 50-100 uM. They look
 like trapezoid crystal. My problem is all of my crystals have not
 diffraction in home source X-ray and just poor diffraction at
 Synchrotron (lower than 20 A). My crystals like to appear on the
 surface of the drop. Look like my crystals are quite light.  I had
 tried to use a needle to touch them. Unlike other protein crystal, my
 crystal looks like quite soft. When I touch it, it didn't crack, but
 was bend or mashed.  I had tried to do additive screen and detergent
 screen. It seems they are not useful.
 
 Do anyone have good ideas to optimization these crystals? Thanks for
 your suggestions.
 
 Frank
 20130917020056875.jpg

Dr. Susanne Ressl
Otto Hahn Fellow of the Max-Planck Society
Stanford University
School of Medicine
James H. Clark Center
318 Campus Drive, Room E300
Stanford, CA 94305-5432
Phone: +1-650-736-1715









Re: [ccp4bb] membrane protein optimization

2013-10-23 Thread Daniel Picot

Hi Frank,
Do not forget that membrane protein crystals are often fragile and 
difficult to manipulate.
Finding good cryo condition can be difficult and small temperature 
variation can destroy crystals
within minutes, this makes room temperature diffraction tests not always 
obvious. The time of harvest may also be critical. In addition to the 
previous suggestions, it is often usefull to check if there is  a large 
amount of lipids in the sample. This can often easily be done by thin 
layer chromatography.

HTH
Daniel


Le 23/10/2013 18:22, crystalboy a écrit :

Hi CCP4BB Forks,

In recently I got a membrane protein crystal in the quite normal
membrane protein crystallization conditions as other persons reported,
like PEG400 16-19%, pH 6.0-7.5, with 50 mM MgCl2 (in my case) by using
sitting drop method. These crystals are around 50-100 uM. They look
like trapezoid crystal. My problem is all of my crystals have not
diffraction in home source X-ray and just poor diffraction at
Synchrotron (lower than 20 A). My crystals like to appear on the
surface of the drop. Look like my crystals are quite light.  I had
tried to use a needle to touch them. Unlike other protein crystal, my
crystal looks like quite soft. When I touch it, it didn't crack, but
was bend or mashed.  I had tried to do additive screen and detergent
screen. It seems they are not useful.

Do anyone have good ideas to optimization these crystals? Thanks for
your suggestions.

Frank


Re: [ccp4bb] Error with iMosflm 1.0.7 of CCP4 6.4.0 kit

2013-10-23 Thread Harry Powell

Hi David

Nothing to do with the iMosflm developers. CCP4 has made some changes  
that have caused this error to arise in 6.4.0 on Linux (this is not  
to say that the iMosflm code didn't have the bug, just that it  
doesn't appear with either our own version or with the same version  
distributed with ccp4 6.3.0).


The guys at ccp4 have produced a fix which will be released shortly,  
but they tell me this works;


For now a quick workaround is to add  2@1  after word exit in line  
847 in ccp4-6.4.0/share/ccp4i/imosflm/src/controller.tcl.


--- src/controller.tcl  2012-11-30 20:46:13 +
+++ src/controller.tcl  2013-10-19 08:52:29 +
@@ -844,7 +844,7 @@
# If an executable has been named...
if {$l_executable != } {
# test the executable, by running it
-   if {![catch {exec $l_executable  exit} l_result]} {
+   if {![catch {exec $l_executable  exit 2@1 }  
l_result]} {

if { [regexp -nocase windows $::tcl_platform(os)] } {
set summary_filename [file join $::env(MOSDIR)  
SUMMARY]

#set summary_filename [list $summary_filename]




Of course, my favourite fix is to run the version from our website  
which does not show this bug.


Best wishes


On 23 Oct 2013, at Wed23 Oct 17:39, David Schuller wrote:


iMosflm developers:

I have installed CCP4 6.4.0, which includes iMosflm 1.0.7 and  
ipmosflm 7.0.9.

This is on Scientific Linux 6.x, 64 bit distribution.

When I run iMosflm either from the command shell or from the ccp4i  
interface, I get an error just like this:

http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg27243.html

iMosflm claims it cannot run without mosflm 7.0.9, followed by  
output indicating that mosflm 7.0.9 runs. (See attached screen  
capture of error message)
Note the linked description is for the previous versions of imosflm  
amd mosflm, so this error seems to be a repeat.


I downloaded the iMosflm and ipmosflm executables from the iMosflm  
web site, put ipmosflm in my executable directory, and this seems  
to fix the problem.


You should get the CCP4 folks to investigate this and propagate a fix.

Cheers,

--
== 
=

 All Things Serve the Beam
== 
=

   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

imosf.err.jpg


Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick  
Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9  
(Crystallographic Computing)







Re: [ccp4bb] membrane protein optimization

2013-10-23 Thread El Arnaout, Toufic
Hi Frank,
The previous suggestions are great. In my case, I had soft crystals (bend from 
180° to ~130-140°) in the loop using the LCP but they still diffracted. There 
are a lot of heroic stories on how some people solved a structure, you should 
just try as many ways as possible (do not only rely for a long time on only one 
condition or construct), and remember methods are just methods (i.e., there 
are hundreds of LCP robots in the world..). Protein engineering, homologs 
(maybe hyperthermophiles).. stabilization.. are great ways.
Recently I had tested various crystals grown by vapor diffusion for a protein 
purified in different ways/detergents, so obtaining crystals is very common, 
but it's just the start. I also had crystals using bicelles but saw huge spots 
to 2 A (no patterns.. rather looked like detergent/lipid).
Good luck

toufic el arnaout





From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of crystalboy 
[yyb...@gmail.com]
Sent: Wednesday, October 23, 2013 11:22 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] membrane protein optimization

Hi CCP4BB Forks,

In recently I got a membrane protein crystal in the quite normal
membrane protein crystallization conditions as other persons reported,
like PEG400 16-19%, pH 6.0-7.5, with 50 mM MgCl2 (in my case) by using
sitting drop method. These crystals are around 50-100 uM. They look
like trapezoid crystal. My problem is all of my crystals have not
diffraction in home source X-ray and just poor diffraction at
Synchrotron (lower than 20 A). My crystals like to appear on the
surface of the drop. Look like my crystals are quite light.  I had
tried to use a needle to touch them. Unlike other protein crystal, my
crystal looks like quite soft. When I touch it, it didn't crack, but
was bend or mashed.  I had tried to do additive screen and detergent
screen. It seems they are not useful.

Do anyone have good ideas to optimization these crystals? Thanks for
your suggestions.

Frank


Re: [ccp4bb] membrane protein optimization

2013-10-23 Thread Emmanuel Doh Nji
Dear Frank,
Toufic is right. The trick is no trick, you just have to try everything. In
my experience if u have a protein crystals in a mild detergent and it is
very fragile no point going to a harsh or shorter chain detergent like OG.
I got crystals in NM (9 C) and they were fragile and dissolved after 1 day.
I could only get stable crystals when I moved to DM (10 C) and DDM (12 C).
Once you get a stable crystal you may consider dehydrating them in higher
PEG so as to improve protein protein contact. Again the trick is no trick,
you just try everything suggested.
Good luck with your trials.
Emmanuel Nji.


On 23 October 2013 19:46, El Arnaout, Toufic
elarnao...@biochem.wustl.eduwrote:

 Hi Frank,
 The previous suggestions are great. In my case, I had soft crystals (bend
 from 180° to ~130-140°) in the loop using the LCP but they still
 diffracted. There are a lot of heroic stories on how some people solved a
 structure, you should just try as many ways as possible (do not only rely
 for a long time on only one condition or construct), and remember methods
 are just methods (i.e., there are hundreds of LCP robots in the world..).
 Protein engineering, homologs (maybe hyperthermophiles).. stabilization..
 are great ways.
 Recently I had tested various crystals grown by vapor diffusion for a
 protein purified in different ways/detergents, so obtaining crystals is
 very common, but it's just the start. I also had crystals using bicelles
 but saw huge spots to 2 A (no patterns.. rather looked like
 detergent/lipid).
 Good luck

 toufic el arnaout




 
 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of crystalboy
 [yyb...@gmail.com]
 Sent: Wednesday, October 23, 2013 11:22 AM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] membrane protein optimization

 Hi CCP4BB Forks,

 In recently I got a membrane protein crystal in the quite normal
 membrane protein crystallization conditions as other persons reported,
 like PEG400 16-19%, pH 6.0-7.5, with 50 mM MgCl2 (in my case) by using
 sitting drop method. These crystals are around 50-100 uM. They look
 like trapezoid crystal. My problem is all of my crystals have not
 diffraction in home source X-ray and just poor diffraction at
 Synchrotron (lower than 20 A). My crystals like to appear on the
 surface of the drop. Look like my crystals are quite light.  I had
 tried to use a needle to touch them. Unlike other protein crystal, my
 crystal looks like quite soft. When I touch it, it didn't crack, but
 was bend or mashed.  I had tried to do additive screen and detergent
 screen. It seems they are not useful.

 Do anyone have good ideas to optimization these crystals? Thanks for
 your suggestions.

 Frank




-- 
Dr. Emmanuel Nji
Department of Biochemistry and Biophysics
Centre for Biomembrane Research
Stockholm University
106 91 Stockholm
Sweden
Cell: 0046736457727


[ccp4bb] MacBook Pro graphics card options

2013-10-23 Thread Kristin Low
Hi everyone,

Sorry for being a bit off topic, but I thought this group would be great for 
advice.

I’m looking at upgrading my current laptop to a newer MacBook Pro. I’m torn as 
to whether I need integrated vs discrete graphics for structural biology, 
including molecular modelling, especially since the latest advances by Intel in 
terms of integrated graphics. Right now with the new releases, the options are 
between Intel Iris Pro (5200 series) and Intel Iris Pro + Nvidia GT 750M. 
Thoughts?


Thanks everyone!

Kristin


-
Kristin Low
Ph.D. Candidate
Queen's University
Department of Biomedical and Molecular Sciences
Botterell Hall, Room 645
Kingston, ON
Canada  K7L 3N6

tel: +1-613-533-3019
-



Re: [ccp4bb] MacBook Pro graphics card options - what about Mavericks?

2013-10-23 Thread Carlos Kikuti
Hi,

Can I profit from Kristin's question and add one: is it too soon to know if the 
crystallography software (CCP4, Coot, Autobuster, XDS) will work fine with 
Mavericks (Mac OS X 10.9)? 

(I remember a bit of trouble when Lion came off).

Carlos

Em 23 oct. 2013, às 22:10, Kristin Low kristin@queensu.ca escreveu:

 Hi everyone,
 
 Sorry for being a bit off topic, but I thought this group would be great for 
 advice.
 
 I’m looking at upgrading my current laptop to a newer MacBook Pro. I’m torn 
 as to whether I need integrated vs discrete graphics for structural biology, 
 including molecular modelling, especially since the latest advances by Intel 
 in terms of integrated graphics. Right now with the new releases, the options 
 are between Intel Iris Pro (5200 series) and Intel Iris Pro + Nvidia GT 750M. 
 Thoughts?
 
 
 Thanks everyone!
 
 Kristin
 
 
 -
 Kristin Low
 Ph.D. Candidate
 Queen's University
 Department of Biomedical and Molecular Sciences
 Botterell Hall, Room 645
 Kingston, ON
 Canada  K7L 3N6
 
 tel: +1-613-533-3019
 -
 



Re: [ccp4bb] MacBook Pro graphics card options - what about Mavericks?

2013-10-23 Thread Francis Reyes
I'm currently using CCP4/COOT (from the official installer) and autoPROC  on 
Mavericks without any problems. I imagine the rest of the global phasing tools 
will work nicely. 


I had issues with fink, you have to use a branch from github as well as 
manually install and update the Command Line Tools just to get fink working...


F

-
Francis E. Reyes PhD
215 UCB
University of Colorado at Boulder
On Oct 23, 2013, at 3:16 PM, Carlos Kikuti kik...@gmail.com wrote:

 Hi,
 
 Can I profit from Kristin's question and add one: is it too soon to know if 
 the crystallography software (CCP4, Coot, Autobuster, XDS) will work fine 
 with Mavericks (Mac OS X 10.9)? 
 
 (I remember a bit of trouble when Lion came off).
 
 Carlos
 
 Em 23 oct. 2013, às 22:10, Kristin Low kristin@queensu.ca escreveu:
 
 Hi everyone,
 
 Sorry for being a bit off topic, but I thought this group would be great for 
 advice.
 
 I’m looking at upgrading my current laptop to a newer MacBook Pro. I’m torn 
 as to whether I need integrated vs discrete graphics for structural biology, 
 including molecular modelling, especially since the latest advances by Intel 
 in terms of integrated graphics. Right now with the new releases, the 
 options are between Intel Iris Pro (5200 series) and Intel Iris Pro + Nvidia 
 GT 750M. Thoughts?
 
 
 Thanks everyone!
 
 Kristin
 
 
 -
 Kristin Low
 Ph.D. Candidate
 Queen's University
 Department of Biomedical and Molecular Sciences
 Botterell Hall, Room 645
 Kingston, ON
 Canada  K7L 3N6
 
 tel: +1-613-533-3019
 -
 
 


Re: [ccp4bb] Error with iMosflm 1.0.7 of CCP4 6.4.0 kit

2013-10-23 Thread Andreas Förster

Hi David,

I've just renamed the ipmosflm in $CCP4/bin to ipmosflm_new and then 
defined


MOSFLM_EXEC as /path/to/ccp4-6.3.0/bin/ipmosflm.

CCP4 6.3 needs to be installed for this to work.


Andreas



On 23/10/2013 5:39, David Schuller wrote:

iMosflm developers:

I have installed CCP4 6.4.0, which includes iMosflm 1.0.7 and ipmosflm
7.0.9.
This is on Scientific Linux 6.x, 64 bit distribution.

When I run iMosflm either from the command shell or from the ccp4i
interface, I get an error just like this:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg27243.html

iMosflm claims it cannot run without mosflm 7.0.9, followed by output
indicating that mosflm 7.0.9 runs. (See attached screen capture of error
message)
Note the linked description is for the previous versions of imosflm amd
mosflm, so this error seems to be a repeat.

I downloaded the iMosflm and ipmosflm executables from the iMosflm web
site, put ipmosflm in my executable directory, and this seems to fix the
problem.

You should get the CCP4 folks to investigate this and propagate a fix.

Cheers,



--
  Andreas Förster
 Crystallization and Xray Facility Manager
   Centre for Structural Biology
  Imperial College London


Re: [ccp4bb] MacBook Pro graphics card options

2013-10-23 Thread Nat Echols
On Wed, Oct 23, 2013 at 1:10 PM, Kristin Low kristin@queensu.ca wrote:

 I’m looking at upgrading my current laptop to a newer MacBook Pro. I’m
 torn as to whether I need integrated vs discrete graphics for structural
 biology, including molecular modelling, especially since the latest
 advances by Intel in terms of integrated graphics. Right now with the new
 releases, the options are between Intel Iris Pro (5200 series) and Intel
 Iris Pro + Nvidia GT 750M.


It depends on how demanding your graphics needs are.  I have no experience
with the Iris Pro chips, but I've been using a MacBook Air from late 2011
almost exclusively for most of the last two years, including heavy use of
Coot and PyMOL, and the only times I've been annoyed by slow graphics is
when I'm trying to visualize a very large and/or high-resolution region of
density.  And even that doesn't happen too often.  Most of the time it runs
very smoothly.  However, there are some persistent glitches with the
graphical display in Coot - sometimes I get weird visual artifacts, or
messed up depth perception.  Whether this is the fault of Coot, XQuartz, or
Intel is unknown.  But speed is not an issue.

The premium for the model with the Nvidia chip is quite steep at $600
(perhaps it's less with academic discount?).  I don't think the graphics
upgrade alone is worth it - but I'd be very tempted by the faster
processor, doubled memory, and doubled SSD, all of which will come in handy
when refining or rendering.

Disclaimer: I know absolutely nothing about the availability of stereo
options with any of these systems.  It's possible the NVidia card has
additional capabilities in that respect.

-Nat